Bioinformatics

Bioinformatics

Like other high throughput technologies such as genechip arrays, proteomics can easily produce millions of data points per experiment that have to be analysed and interpreted. This information is of little or no value unless it is presented to researchers in the proper context and in connection with other mainly biological information. This is where bioinformatics plays an important role.

 

Firstly, we provide bioinformatics support in the identification and quantification of proteins and phospho-peptides from mass spectrometric data, using both our in-house tools and commercial software tools, including Mascot and ProteinPilot (Applied Biosystems).

We are developing a web-based viewer for proteomics data. Improved methods for interrogating and comparing datasets are being developed to help in finding the best and most interesting results.

The LRF Proteomics group was involved in the development of the PEDRo data model for the storage and dissemination of proteomic data developed by colleagues at the University of Manchester (Taylor et al., Nature Biotech, 2003).

The Bioinformatics group at the Paterson Institute for Cancer Research led by Dr Crispin Miller is collaborating closely to provide bioinformatics support. They have considerable expertise in the field of proteome bioinformatics and in collaboration with the LRF proteomics facility have implemented bioinformatics techniques to successfully integrate proteomics data with microarray based approaches.

Related Publications

Unwin RD, Smith DL, Blinco D, Wilson CL, Miller CJ, Evans CA, Jaworska E, Baldwin SA, Barnes K, Pierce A, Spooncer E, Whetton AD (15 Jun 2006) Quantitative proteomics reveals posttranslational control as a regulatory factor in primary hematopoietic stem cells. in Blood v.107 i.12 - 4687-94

Gel Image Analysis

  • Progenesis
  • Phoretix 2D Database software
  • Spot Excision/ Enzymatic Digestion of Proteins
    Manual/automated spot picking/digestion